Analysis of Self-Cleaving Ribozyme Transition States

Endonucleolytic ribozymes, non-coding RNA molecules capable of self-scission, have been studied for decades. First, because of their novel functionality, and later because their capacity to serve as paradigmatic model systems of RNA catalysis. Nine classes of endonucleolytic have been described to-date, and all facilitate cleavage through the same set of catalytic strategies: nucleophile activation, leaving group protonation, electrostatic stabilization, and active site organization. However, the chemical tools employed to engage these strategies varies widely between ribozyme classes. Whether or not differences between ribozyme active sites can meaningfully alter reaction pathways remains an open question with important implications for ribozyme evolution and biological catalysis. In this work, I describe the network of chemical interactions that organize the Varkud Satellite ribozyme active site and use biophysical methods to characterize the transition state for the hepatitis delta virus ribozyme. Together, these data provide clarity on the catalytic strategies engaged by ribozyme active sites and the degree to which biological catalysts can alter reaction pathways.